6-31480377-A-G

Position:

• chr6-31480377-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_149132.1(MICB-DT):​n.1523T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,752 control chromosomes in the GnomAD database, including 30,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (30040 hom., cov: 32)
• Consequence: MICB-DT NR_149132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

Genes affected

MICB-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MICB-DT	NR_149132.1	n.1523T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICB-DT	ENST00000665353.1	n.1664T>C		non_coding_transcript_exon_variant	2/2
MICB-DT	ENST00000656299.1	n.1000T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94478 AN: 151634 Hom.: 29989 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.623 AC: 94575 AN: 151752 Hom.: 30040 Cov.: 32 AF XY: 0.627 AC XY: 46498 AN XY: 74184

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.611

Alfa AF: 0.636 Hom.: 41930

Bravo AF: 0.625

Asia WGS AF: 0.696 AC: 2422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2523651; hg19: chr6-31448154;